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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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MDA-MB-361 breast adenocarcinoma cells treated in vitro with allosteric AKT inhibitor MK2206 until development of resistance.

ABSTRACT: Whole exome sequencing to determine whether acquisition of resistance to MK2206 in MDA-MB-361 is mediated by a new AKT1 mutation. Cells were exposed in vitro to drug for 12 weeks. Surviving cells were expanded for another 2 weeks in the presence of drug before sequencing.

INSTRUMENT(S): HiSeq X Ten

ORGANISM(S): Homo sapiens

SUBMITTER: NICOLAOS PALASKAS

PROVIDER: E-MTAB-8066 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Massive parallel sequencing uncovers actionable FGFR2-PPHLN1 fusion and ARAF mutations in intrahepatic cholangiocarcinoma

Project description:Intrahepatic cholangiocarcinoma (iCCA) is a fatal bile duct cancer with dismal prognosis and limited therapeutic options. By performing RNA- and exome sequencing analyses we have discovered a novel fusion event, FGFR2-PPHLN1 (16%), and damaging mutations in the ARAF oncogene (11%). Methods: mRNA and gDNA were exctracted from fresh frozen tumor tissues and corresponding normal tissue (n=8 pairs) from patients with iCCA who underwent surgical resection. RNA-seq was performed using Illumina HiSeq 2500 System with 100 nucleotide single-end reads. One sample and its paired non-tumoral tissue were eliminated from the subsequent analysis because of bad RNa quality. The same 8 paired tumors were also analyzed by whole-exome seq. Submitter confirms there are no patient privacy concerns with these data. This dataset is part of the TransQST collection.

2015-01-22 | E-GEOD-63420 | biostudies-arrayexpress

Correction of human phospholamban R14del mutation associated with cardiomyopathy using targeted nucleases and combination therapy [Exome-Seq]

Project description:Phospholamban R14del mutazion (PLN-R14del) has been identified in a large family pedigree in which heterozygous carriers exhibited inherited dilated cardiomyopathy (DCM) and death by middle age. To better understand the causal link between the mutations in PLN and DCM pathology, we derived induced pluripotent stem cells from a DCM patient carrying the PLN R14del mutation. We showed that iPSC-derived cardiomyocytes recapitulated the DCM-specific phenotype and demonstrated that either TALEN-mediated genetic correction or combinatorial gene therapy resulted in phenotypic rescue. Our findings offer novel insights into the pathogenesis caused by mutant PLN and point to the development of potential new therapeutics of pathogenic genetic variants associated with inherited cardiomyopathies. Submitter confirms there are no patient privacy concerns with these data. iPSCs were derived from a female patient carrying a heterozygous mutation (R14del) in the PLN gene. Tree samples were analyzed: R14del-CMs (clone L2), corrected R14del-CMs (clone L2GC1) and corrected R14del-CMs (clone L2GC2)

2015-02-09 | E-GEOD-65762 | biostudies-arrayexpress

Effects of MDMA and Venlafaxine treatment in Dark Agouti rats

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2013-06-01 | E-GEOD-47541 | biostudies-arrayexpress

Identification of protein-protein interaction mediated by N-myristoylated proteins using photocrosslinkable clickable myristoylation probes X3 and X10

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2023-02-04 | PXD029944 | Pride

Effects of PGRMC1 phosphorylation on genome integrity and epigenetics

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2019-12-01 | E-MTAB-8218 | biostudies-arrayexpress

C9ORF72 GGGGCC expanded repeats produce splicing dysregulation which correlates with disease severity in amyotrophic lateral sclerosis

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-05-08 | E-GEOD-68608 | biostudies-arrayexpress

Proteogenomics of malignant melanoma cell lines: searching for genetically encoded point mutations in LC-MS/MS data

Project description:In this study we performed proteogenomic analysis for 9 cell lines of malignant melanoma. The main objectives of the study were identifying the variants originating from point mutations and analyzing the effect of exome data filtering on the outcome of variant identification.

2018-12-05 | PXD007662 | Pride

Mass spectrometry analysis of the blood plasma and serum samples from healthy donors

Project description:Previously, we published a dataset of human blood plasma and serum samples of 10 healthy males and 10 healthy females, fractionated on a set of sorbents (cation exchange Toyopearl CM-650M, CM Bio-Gel A, SP Sephadex C-25 and anion exchange QAE Sephadex A-25) and analyzed by LC-MS/MS individually and pooled in equal amounts (Supplementary Table S1, Sheet 1) [33]. We focused on those peptides that could be found in the blood plasma and serum using a standard search against the database of human proteins (UniProt Knowledgebase, taxon human). The combination of search engines MASCOT and X! Tandem, based on Scaffold 4 software with FDR less than 1%, allowed us to identify 15,530 unique peptides that belong to 2,127 protein groups (Table 1, Supplementary Table S1, Sheets 2 and 3). The Venn diagram shows that slightly less than 40% of the peptides are found in all four analyzed samples (Figures 1A and 1B). About 70% of the peptides are found in at least two samples. The accumulation diagram (Figure 1C) shows that the number of new unique peptides does not reach a plateau after repeated analyses of the same plasma sample — even after six runs. The high variability of the plasma and serum peptidome most likely indicates its sophisticated composition. 33. Arapidi, G. et al. Peptidomics dataset: Blood plasma and serum samples of healthy donors fractionated on a set of chromatography sorbents. Data Brief 18, 1204–1211 (2018).

2024-06-14 | PXD027552 | Pride

C9ORF72 GGGGCC expanded repeats produce splicing dysregulation which correlates with disease severity in amyotrophic lateral sclerosis [HG-U133_Plus_2]

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2015-05-08 | E-GEOD-68605 | biostudies-arrayexpress

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2024-08-31 | E-MTAB-14350 | biostudies-arrayexpress

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